4L7D

Structure of keap1 kelch domain with (1S,2R)-2-{[(1S)-5-methyl-1-[(1-oxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid

• PDB DOI:  https://doi.org/10.2210/pdb4L7D/pdb

• Classification: TRANSCRIPTION/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-06-13 Released: 2014-02-19 
• Deposition Author(s): Jnoff, E., Brookfield, F., Albrecht, C., Barker, J.J., Barker, O., Beaumont, E., Bromidge, S., Brooks, M., Ceska, T., Courade, J.P., Crabbe, T., Duclos, S., Fryatt, T., Jigorel, E., Kwong, J., Sands, Z., Smith, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.276 
• R-Value Work: 0.252 
• R-Value Observed: 0.253 

Literature

Binding Mode and Structure-Activity Relationships around Direct Inhibitors of the Nrf2-Keap1 Complex.

Jnoff, E., Albrecht, C., Barker, J.J., Barker, O., Beaumont, E., Bromidge, S., Brookfield, F., Brooks, M., Bubert, C., Ceska, T., Corden, V., Dawson, G., Duclos, S., Fryatt, T., Genicot, C., Jigorel, E., Kwong, J., Maghames, R., Mushi, I., Pike, R., Sands, Z.A., Smith, M.A., Stimson, C.C., Courade, J.P.

(2014) ChemMedChem 9: 699-705

• PubMed: 24504667 
• DOI: https://doi.org/10.1002/cmdc.201300525
• Primary Citation of Related Structures:  
  4L7B, 4L7C, 4L7D, 4N1B


• PubMed Abstract: 
  

An X-ray crystal structure of Kelch-like ECH-associated protein (Keap1) co-crystallised with (1S,2R)-2-[(1S)-1-[(1,3-dioxo-2,3-dihydro-1H-isoindol-2-yl)methyl]-1,2,3,4-tetrahydroisoquinolin-2-carbonyl]cyclohexane-1-carboxylic acid (compound (S,R,S)-1 a) was obtained. This X-ray crystal structure provides breakthrough experimental evidence for the true binding mode of the hit compound (S,R,S)-1 a, as the ligand orientation was found to differ from that of the initial docking model, which was available at the start of the project. Crystallographic elucidation of this binding mode helped to focus and drive the drug design process more effectively and efficiently.

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Organizational Affiliation: 

UCB Pharma, UCB NewMedicines, Chemin du Foriest, 1420 Braine-l'Alleud (Belgium). [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 100.96 kDa 
• Atom Count: 7,081 
• Modelled Residue Count: 858 
• Deposited Residue Count: 900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A, B, C	300	Homo sapiens	Mutation(s): 1  Gene Names: KEAP1, INRF2, KIAA0132, KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens) Explore Q14145  Go to UniProtKB:  Q14145
PHAROS:  Q14145

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1VX	D [auth A], G [auth B], K [auth C]	(1S,2R)-2-{[(1S)-5-methyl-1-[(1-oxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid C27 H30 N2 O4 YTUXAQFRBNUADX-TZRRMPRUSA-N
ACT	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
1VX	Binding MOAD:  4L7D	IC50: 750 (nM) from 1 assay(s)
	BindingDB:  4L7D	IC50: 750 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.276 
• R-Value Work: 0.252 
• R-Value Observed: 0.253 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.92	α = 90
b = 126	β = 90
c = 130.3	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Jnoff, E., Brookfield, F., Albrecht, C., Barker, J.J., Barker, O., Beaumont, E., Bromidge, S., Brooks, M., Ceska, T., Courade, J.P., Crabbe, T., Duclos, S., Fryatt, T., Jigorel, E., Kwong, J., Sands, Z., Smith, M.A.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2014-04-23
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description